Buggy code:
public class RealMatrixImpl implements Serializable , RealMatrix { private static final long serialVersionUID = - 4828886979278117018L ; protected double [ ] [ ] data = null ; protected double [ ] [ ] lu = null ; protected int [ ] permutation = null ; protected int parity = 1 ; private static final double TOO_SMALL = 1.0E-11 ; public RealMatrixImpl ( ) { } public RealMatrixImpl ( int rowDimension , int columnDimension ) { } public RealMatrixImpl ( double [ ] [ ] d ) { } public RealMatrixImpl ( double [ ] [ ] d , boolean copyArray ) { } public RealMatrixImpl ( double [ ] v ) { } public RealMatrix copy ( ) { } public RealMatrix add ( RealMatrix m ) throws IllegalArgumentException { } public RealMatrixImpl add ( RealMatrixImpl m ) throws IllegalArgumentException { } public RealMatrix subtract ( RealMatrix m ) throws IllegalArgumentException { } public RealMatrixImpl subtract ( RealMatrixImpl m ) throws IllegalArgumentException { } public RealMatrix scalarAdd ( double d ) { } public RealMatrix scalarMultiply ( double d ) { } public RealMatrix multiply ( RealMatrix m ) throws IllegalArgumentException { } public RealMatrixImpl multiply ( RealMatrixImpl m ) throws IllegalArgumentException { } public RealMatrix preMultiply ( RealMatrix m ) throws IllegalArgumentException { } public double [ ] [ ] getData ( ) { } public double [ ] [ ] getDataRef ( ) { } public double getNorm ( ) { } public RealMatrix getSubMatrix ( int startRow , int endRow , int startColumn , int endColumn ) throws MatrixIndexException { } public RealMatrix getSubMatrix ( int [ ] selectedRows , int [ ] selectedColumns ) throws MatrixIndexException { } public void setSubMatrix ( double [ ] [ ] subMatrix , int row , int column ) throws MatrixIndexException { } public RealMatrix getRowMatrix ( int row ) throws MatrixIndexException { } public RealMatrix getColumnMatrix ( int column ) throws MatrixIndexException { } public double [ ] getRow ( int row ) throws MatrixIndexException { } public double [ ] getColumn ( int col ) throws MatrixIndexException { } public double getEntry ( int row , int column ) throws MatrixIndexException { } public RealMatrix transpose ( ) { } public RealMatrix inverse ( ) throws InvalidMatrixException { } public double getDeterminant ( ) throws InvalidMatrixException { } public boolean isSquare ( ) { } public boolean isSingular ( ) { } public int getRowDimension ( ) { } public int getColumnDimension ( ) { } public double getTrace ( ) throws IllegalArgumentException { } public double [ ] operate ( double [ ] v ) throws IllegalArgumentException { final int nRows = this . getRowDimension ( ) ; final int nCols = this . getColumnDimension ( ) ; if ( ( v . length ) != nCols ) { throw new IllegalArgumentException ( "vector<seq2seq4repair_space>has<seq2seq4repair_space>wrong<seq2seq4repair_space>length" ) ; } <START_BUG> final double [ ] out = new double [ v . length ] ; <END_BUG> for ( int row = 0 ; row < nRows ; row ++ ) { final double [ ] dataRow = data [ row ] ; double sum = 0 ; for ( int i = 0 ; i < nCols ; i ++ ) { sum += ( dataRow [ i ] ) * ( v [ i ] ) ; } out [ row ] = sum ; } return out ; } public double [ ] preMultiply ( double [ ] v ) throws IllegalArgumentException { } public double [ ] solve ( double [ ] b ) throws IllegalArgumentException , InvalidMatrixException { } public RealMatrix solve ( RealMatrix b ) throws IllegalArgumentException , InvalidMatrixException { } public void luDecompose ( ) throws InvalidMatrixException { } public String toString ( ) { } public boolean equals ( Object object ) { } public int hashCode ( ) { } protected RealMatrix getLUMatrix ( ) throws InvalidMatrixException { } protected int [ ] getPermutation ( ) { } private double [ ] [ ] copyOut ( ) { } private void copyIn ( double [ ] [ ] in ) { } private boolean isValidCoordinate ( int row , int col ) { } }

Fix:
final double [ ] out = new double [ nRows ] ;